ABSTRACT The use of molecular epidemiology and population genetics has revolutionized the ways in which we study infectious diseases and, in particular, pathogen diversity. This revolution has been facilitated by the explosive increase in available genetic data, primarily due to second-generation sequencing. Treponema pallidum subsp. pallidum (TPA) genetic data will play an integral role in the completion of all three CRC Projects. To ensure the quality and robustness of this data across projects, the CRC will support the UNC/Masaryk University Genetics and Genomics Core (GGC). The GGC is a multi-institution core, led by the University of North Carolina, that is designed to enable the CRC to apply state-of-the-art, next-generation sequencing, and bioinformatic tools to catalog the sequence diversity of TPA outer membrane proteins (OMPs). Categorization of this diversity is necessary for developing a broadly protective, globally effective syphilis vaccine using immunogenic OMPs as vaccine antigens. In order to support TPA vaccine development, the GGC will: 1) provide laboratory support for genetic analysis of clinical isolates in order to define the diversity of the TPA ?OMPeome?, 2) provide bioinformatic processing and data management for the CRC, including generating cleaned data to all the CRC Projects for analysis and disseminating this data to the scientific community, 3) train CRC investigators in genomic methods and facilitate cross-CRC training, and 4) develop novel tools to advance TPA genomics. The GGC has developed: 1) a detailed plan to ensure efficient collaboration between the core and CRC Projects, 2) processes to ensure the rigor and reproducibility of the data, and 3) plans for the dissemination of data, bioinformatic tools and laboratory methods to the scientific community.